#setwd('/afs/inf.ed.ac.uk/user/s17/s1725186/Documents/PhD-Models/FirstPUModel/RMarkdowns')

library(tidyverse) ; library(reshape2) ; library(glue) ; library(plotly) ; library(dendextend)
library(RColorBrewer) ; library(viridis) ; require(gridExtra) ; library(GGally)
library(knitr)
library(biomaRt)
library(clusterProfiler) ; library(ReactomePA) ; library(DOSE)

Load preprocessed dataset (preprocessing code in 19_10_14_data_preprocessing.Rmd) and clustering (pipeline in 19_10_21_WGCNA.Rmd)

# Gandal dataset
load('./../Data/preprocessed_data.RData')
datExpr = datExpr %>% data.frame
DE_info = DE_info %>% data.frame


# GO Neuronal annotations: regex 'neuron' in GO functional annotations and label the genes that make a match as neuronal
GO_annotations = read.csv('./../Data/genes_GO_annotations.csv')
GO_neuronal = GO_annotations %>% filter(grepl('neuron', go_term)) %>% 
              mutate('ID'=as.character(ensembl_gene_id)) %>% 
              dplyr::select(-ensembl_gene_id) %>% distinct(ID) %>%
              mutate('Neuronal'=1)


# SFARI Genes
SFARI_genes = read_csv('./../../../SFARI/Data/SFARI_genes_01-03-2020_w_ensembl_IDs.csv')
SFARI_genes = SFARI_genes[!duplicated(SFARI_genes$ID) & !is.na(SFARI_genes$ID),]


# Clusterings
clusterings = read_csv('./../Data/clusters.csv')


# Update DE_info with SFARI and Neuronal information
genes_info = DE_info %>% mutate('ID'=rownames(.)) %>% left_join(SFARI_genes, by='ID') %>% 
  mutate(`gene-score`=ifelse(is.na(`gene-score`), 'None', `gene-score`)) %>%
  left_join(GO_neuronal, by='ID') %>% left_join(clusterings, by='ID') %>%
  mutate(Neuronal=ifelse(is.na(Neuronal), 0, Neuronal)) %>%
  mutate(gene.score=ifelse(`gene-score`=='None' & Neuronal==1, 'Neuronal', `gene-score`), 
         significant=padj<0.05 & !is.na(padj))


clustering_selected = 'DynamicHybrid'
genes_info$Module = genes_info[,clustering_selected]

dataset = read.csv(paste0('./../Data/dataset_', clustering_selected, '.csv'))
dataset$Module = dataset[,clustering_selected]

# Correct SFARI Scores
dataset$gene.score = genes_info$gene.score

# GSEA Results
load('./../Data/GSEA_bonferroni.RData')


SFARI_colour_hue = function(r) {
  pal = c('#FF7631','#FFB100','#E8E328','#8CC83F','#62CCA6','#59B9C9','#b3b3b3','#808080','gray','#d9d9d9')[r]
}

rm(DE_info, GO_annotations, clusterings, getinfo, mart, dds, GO_neuronal)


Module-Diagnosis Correlation

plot_data = dataset %>% dplyr::select(Module, MTcor) %>% distinct

ggplotly(plot_data %>% ggplot(aes(reorder(Module, -MTcor), MTcor)) + geom_bar(stat='identity', fill = plot_data$Module) + theme_minimal() + 
         xlab('Modules')+ ylab('Module-Diagnosis Correlation') + geom_hline(yintercept =c(0.9, -0.9), color = 'gray', linetype = 'dashed') + 
         theme(axis.text.x = element_text(angle = 90, hjust = 1)))
top_modules = plot_data %>% arrange(desc(MTcor)) %>% filter(abs(MTcor)>0.9) %>% dplyr::pull(Module) %>% 
              unique %>% as.character

cat(paste0('Top modules selected: ', paste(top_modules, collapse=', '),'\n'))
## Top modules selected: #73B000, #EE8045, #00B9E3, #84AD00
print_results = function(enrichment_list){
  
  for(module in top_modules){
    
    df = enrichment_list[[module]] %>% dplyr::select(ID, Description, setSize, NES, p.adjust, qvalues) %>% 
         arrange(desc(NES)) %>% filter(NES>0, p.adjust<0.05)
    
    if(nrow(df)>0){
      
      print(kable(df, caption = paste0('Enriched terms for module ', module, ' (MTcor = ', 
                                       round(dataset$MTcor[dataset$Module==module][1],2),')')))
      cat('\n') 
    
    } else {
      df = enrichment_list[[module]] %>% dplyr::select(ID, Description, setSize, NES, p.adjust, qvalues) %>% 
            arrange(desc(NES)) %>% filter(p.adjust<0.05)
      
      if(nrow(df)>0){
        
        print(kable(df, caption = paste0('Negatively Enriched terms for module ', module, ' (MTcor = ', 
                                         round(dataset$MTcor[dataset$Module==module][1],2),')')))
        cat('\n') 
        
      } else cat(paste0('\nNo enrichment found for module ',module,'\n'))
    }
  }
}


GSEA Results


KEGG

print_results(enrichment_KEGG)
Enriched terms for module #73B000 (MTcor = 0.94)
ID Description setSize NES p.adjust qvalues
hsa05322 Systemic lupus erythematosus 108 3.153606 0.0059327 0.0002077
hsa05034 Alcoholism 165 2.459042 0.0058904 0.0002077
hsa04061 Viral protein interaction with cytokine and cytokine receptor 52 2.281161 0.0060269 0.0002077
hsa05202 Transcriptional misregulation in cancer 163 2.203888 0.0059057 0.0002077
hsa05144 Malaria 39 2.157958 0.0060429 0.0002077
hsa04392 Hippo signaling pathway - multiple species 26 2.125743 0.0241726 0.0005221
hsa05321 Inflammatory bowel disease (IBD) 47 2.112495 0.0120419 0.0003279
hsa05150 Staphylococcus aureus infection 49 2.105556 0.0060243 0.0002077
hsa04064 NF-kappa B signaling pathway 89 2.084849 0.0059586 0.0002077
hsa04060 Cytokine-cytokine receptor interaction 170 2.038993 0.0058959 0.0002077
hsa05203 Viral carcinogenesis 188 1.947256 0.0058775 0.0002077
hsa05205 Proteoglycans in cancer 190 1.767234 0.0176180 0.0004244
hsa05206 MicroRNAs in cancer 155 1.749387 0.0295820 0.0005615
hsa04510 Focal adhesion 192 1.729820 0.0294080 0.0005615
hsa05168 Herpes simplex virus 1 infection 446 1.684611 0.0056711 0.0002077
hsa05131 Shigellosis 229 1.679445 0.0291453 0.0005615
Enriched terms for module #EE8045 (MTcor = 0.93)
ID Description setSize NES p.adjust qvalues
hsa05322 Systemic lupus erythematosus 108 3.116966 0.0051117 0.0002189
hsa05168 Herpes simplex virus 1 infection 446 2.552720 0.0043657 0.0002189
hsa05202 Transcriptional misregulation in cancer 163 2.476862 0.0049160 0.0002189
hsa05150 Staphylococcus aureus infection 49 2.470281 0.0054361 0.0002189
hsa05034 Alcoholism 165 2.468803 0.0049104 0.0002189
hsa04064 NF-kappa B signaling pathway 89 2.297403 0.0052044 0.0002189
hsa04610 Complement and coagulation cascades 61 2.180640 0.0053376 0.0002189
hsa05321 Inflammatory bowel disease (IBD) 47 2.167627 0.0054505 0.0002189
hsa04392 Hippo signaling pathway - multiple species 26 2.114051 0.0394716 0.0007043
hsa04061 Viral protein interaction with cytokine and cytokine receptor 52 2.110892 0.0054038 0.0002189
hsa05320 Autoimmune thyroid disease 28 2.106539 0.0224633 0.0004130
hsa05416 Viral myocarditis 52 2.074541 0.0108075 0.0002249
hsa05134 Legionellosis 52 2.069673 0.0162113 0.0003073
hsa05203 Viral carcinogenesis 188 2.006682 0.0048435 0.0002189
hsa04060 Cytokine-cytokine receptor interaction 170 1.967226 0.0049041 0.0002189
hsa04621 NOD-like receptor signaling pathway 148 1.808400 0.0148797 0.0002912
Enriched terms for module #00B9E3 (MTcor = -0.93)
ID Description setSize NES p.adjust qvalues
hsa00190 Oxidative phosphorylation 127 2.755517 0.0047049 0.0001315
hsa05016 Huntington disease 289 2.603602 0.0042150 0.0001315
hsa05012 Parkinson disease 235 2.563026 0.0043358 0.0001315
hsa04723 Retrograde endocannabinoid signaling 142 2.388517 0.0046292 0.0001315
hsa04721 Synaptic vesicle cycle 70 2.379935 0.0050547 0.0001315
hsa05010 Alzheimer disease 348 2.343123 0.0041027 0.0001315
hsa04260 Cardiac muscle contraction 79 2.298468 0.0049764 0.0001315
hsa04970 Salivary secretion 72 2.282474 0.0050353 0.0001315
hsa05033 Nicotine addiction 35 2.280163 0.0054286 0.0001315
hsa04114 Oocyte meiosis 108 2.236445 0.0047818 0.0001315
hsa00020 Citrate cycle (TCA cycle) 29 2.232058 0.0110237 0.0002169
hsa04720 Long-term potentiation 65 2.231082 0.0050997 0.0001315
hsa04728 Dopaminergic synapse 125 2.211123 0.0047074 0.0001315
hsa03050 Proteasome 43 2.188132 0.0053222 0.0001315
hsa04727 GABAergic synapse 82 2.182124 0.0049599 0.0001315
hsa05017 Spinocerebellar ataxia 124 2.165103 0.0047085 0.0001315
hsa04932 Non-alcoholic fatty liver disease (NAFLD) 139 2.162103 0.0046522 0.0001315
hsa04714 Thermogenesis 220 2.150838 0.0043835 0.0001315
hsa04961 Endocrine and other factor-regulated calcium reabsorption 48 2.137410 0.0052562 0.0001315
hsa04713 Circadian entrainment 93 2.128948 0.0048844 0.0001315
hsa04724 Glutamatergic synapse 108 2.106738 0.0095637 0.0002054
hsa04740 Olfactory transduction 76 2.058759 0.0050016 0.0001315
hsa05031 Amphetamine addiction 63 2.055094 0.0051199 0.0001315
hsa05032 Morphine addiction 85 2.045752 0.0049297 0.0001315
hsa04020 Calcium signaling pathway 184 1.969428 0.0044889 0.0001315
hsa04070 Phosphatidylinositol signaling system 95 1.955506 0.0048702 0.0001315
hsa04925 Aldosterone synthesis and secretion 91 1.940975 0.0097879 0.0002054
hsa04929 GnRH secretion 60 1.932295 0.0412067 0.0006634
hsa04261 Adrenergic signaling in cardiomyocytes 141 1.918299 0.0046345 0.0001315
hsa04921 Oxytocin signaling pathway 149 1.917718 0.0045945 0.0001315
hsa04750 Inflammatory mediator regulation of TRP channels 94 1.881673 0.0195223 0.0003414
hsa04725 Cholinergic synapse 106 1.879938 0.0191920 0.0003414
hsa04910 Insulin signaling pathway 130 1.797130 0.0421438 0.0006634
Enriched terms for module #84AD00 (MTcor = -0.93)
ID Description setSize NES p.adjust qvalues
hsa00190 Oxidative phosphorylation 127 2.945789 0.0061467 0.0002020
hsa05016 Huntington disease 289 2.675672 0.0059725 0.0002020
hsa00020 Citrate cycle (TCA cycle) 29 2.597006 0.0063968 0.0002020
hsa05012 Parkinson disease 235 2.585831 0.0060325 0.0002020
hsa04260 Cardiac muscle contraction 79 2.332358 0.0062790 0.0002020
hsa05010 Alzheimer disease 348 2.314316 0.0059151 0.0002020
hsa04721 Synaptic vesicle cycle 70 2.294327 0.0062638 0.0002020
hsa04714 Thermogenesis 220 2.234977 0.0060494 0.0002020
hsa03050 Proteasome 43 2.233015 0.0063597 0.0002020
hsa04932 Non-alcoholic fatty liver disease (NAFLD) 139 2.173141 0.0061074 0.0002020
hsa01210 2-Oxocarboxylic acid metabolism 16 2.134622 0.0259289 0.0006706
hsa01200 Carbon metabolism 109 2.127586 0.0061770 0.0002020
hsa04723 Retrograde endocannabinoid signaling 142 2.098863 0.0061081 0.0002020
hsa04728 Dopaminergic synapse 125 2.012312 0.0061470 0.0002020
hsa04961 Endocrine and other factor-regulated calcium reabsorption 48 2.012073 0.0442044 0.0009997
hsa05017 Spinocerebellar ataxia 124 1.969167 0.0061532 0.0002020
hsa01230 Biosynthesis of amino acids 68 1.967095 0.0376334 0.0009141
hsa04910 Insulin signaling pathway 130 1.918522 0.0061312 0.0002020
hsa04740 Olfactory transduction 76 1.916677 0.0438764 0.0009997
hsa04925 Aldosterone synthesis and secretion 91 1.916531 0.0062171 0.0002020
hsa04261 Adrenergic signaling in cardiomyocytes 141 1.873656 0.0061158 0.0002020
hsa04020 Calcium signaling pathway 184 1.678485 0.0487277 0.0010653

Reactome

print_results(enrichment_Reactome)
Enriched terms for module #73B000 (MTcor = 0.94)
ID Description setSize NES p.adjust qvalues
R-HSA-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 59 3.404989 0.0251148 0.0001590
R-HSA-5334118 DNA methylation 57 3.354489 0.0251134 0.0001590
R-HSA-2299718 Condensation of Prophase Chromosomes 66 3.346491 0.0250763 0.0001590
R-HSA-73728 RNA Polymerase I Promoter Opening 57 3.315263 0.0251134 0.0001590
R-HSA-427359 SIRT1 negatively regulates rRNA expression 62 3.250592 0.0251285 0.0001590
R-HSA-212300 PRC2 methylates histones and DNA 67 3.227406 0.0250861 0.0001590
R-HSA-912446 Meiotic recombination 77 3.195567 0.0250397 0.0001590
R-HSA-1912408 Pre-NOTCH Transcription and Translation 87 3.192122 0.0250673 0.0001590
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression 70 3.166086 0.0251176 0.0001590
R-HSA-1912422 Pre-NOTCH Expression and Processing 103 3.120790 0.0250294 0.0001590
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function 87 3.120711 0.0250673 0.0001590
R-HSA-5625740 RHO GTPases activate PKNs 87 3.100816 0.0250673 0.0001590
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex 83 3.071049 0.0250927 0.0001590
R-HSA-977225 Amyloid fiber formation 92 3.054978 0.0249353 0.0001590
R-HSA-171306 Packaging Of Telomere Ends 45 3.053194 0.0252883 0.0001590
R-HSA-1500620 Meiosis 106 3.047447 0.0249511 0.0001590
R-HSA-2559582 Senescence-Associated Secretory Phenotype (SASP) 103 3.033487 0.0250294 0.0001590
R-HSA-3214815 HDACs deacetylate histones 89 3.027939 0.0250215 0.0001590
R-HSA-110330 Recognition and association of DNA glycosylase with site containing an affected purine 49 3.020401 0.0251918 0.0001590
R-HSA-110331 Cleavage of the damaged purine 49 3.020401 0.0251918 0.0001590
R-HSA-73927 Depurination 49 3.020401 0.0251918 0.0001590
R-HSA-1474165 Reproduction 121 3.018783 0.0249159 0.0001590
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis 105 3.005654 0.0249660 0.0001590
R-HSA-5619507 Activation of HOX genes during differentiation 105 3.005654 0.0249660 0.0001590
R-HSA-73772 RNA Polymerase I Promoter Escape 85 2.995694 0.0250505 0.0001590
R-HSA-9018519 Estrogen-dependent gene expression 139 2.977948 0.0247648 0.0001590
R-HSA-3214842 HDMs demethylate histones 50 2.973280 0.0251648 0.0001590
R-HSA-1221632 Meiotic synapsis 69 2.972464 0.0251148 0.0001590
R-HSA-5250924 B-WICH complex positively regulates rRNA expression 85 2.968917 0.0250505 0.0001590
R-HSA-5578749 Transcriptional regulation by small RNAs 100 2.925635 0.0250196 0.0001590
R-HSA-110328 Recognition and association of DNA glycosylase with site containing an affected pyrimidine 54 2.921933 0.0251435 0.0001590
R-HSA-110329 Cleavage of the damaged pyrimidine 54 2.921933 0.0251435 0.0001590
R-HSA-73928 Depyrimidination 54 2.921933 0.0251435 0.0001590
R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere 67 2.897203 0.0250861 0.0001590
R-HSA-774815 Nucleosome assembly 67 2.897203 0.0250861 0.0001590
R-HSA-73929 Base-Excision Repair, AP Site Formation 56 2.892719 0.0251228 0.0001590
R-HSA-3214858 RMTs methylate histone arginines 74 2.859401 0.0251318 0.0001590
R-HSA-427413 NoRC negatively regulates rRNA expression 100 2.815700 0.0250196 0.0001590
R-HSA-68875 Mitotic Prophase 134 2.803678 0.0248199 0.0001590
R-HSA-5250913 Positive epigenetic regulation of rRNA expression 100 2.789580 0.0250196 0.0001590
R-HSA-2559586 DNA Damage/Telomere Stress Induced Senescence 72 2.789390 0.0251223 0.0001590
R-HSA-5250941 Negative epigenetic regulation of rRNA expression 103 2.768677 0.0250294 0.0001590
R-HSA-73864 RNA Polymerase I Transcription 105 2.759782 0.0249660 0.0001590
R-HSA-73854 RNA Polymerase I Promoter Clearance 104 2.732154 0.0250247 0.0001590
R-HSA-3214841 PKMTs methylate histone lysines 68 2.710487 0.0251059 0.0001590
R-HSA-2559580 Oxidative Stress Induced Senescence 116 2.699026 0.0249135 0.0001590
R-HSA-157579 Telomere Maintenance 74 2.672800 0.0251318 0.0001590
R-HSA-211000 Gene Silencing by RNA 128 2.604248 0.0247987 0.0001590
R-HSA-3214847 HATs acetylate histones 134 2.598060 0.0248199 0.0001590
R-HSA-8939211 ESR-mediated signaling 205 2.590280 0.0244928 0.0001590
R-HSA-73884 Base Excision Repair 84 2.546982 0.0250805 0.0001590
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs 120 2.515455 0.0249302 0.0001590
R-HSA-6785807 Interleukin-4 and Interleukin-13 signaling 88 2.497601 0.0250439 0.0001590
R-HSA-73886 Chromosome Maintenance 101 2.483760 0.0249846 0.0001590
R-HSA-2559583 Cellular Senescence 183 2.480288 0.0246088 0.0001590
R-HSA-212165 Epigenetic regulation of gene expression 140 2.462506 0.0247974 0.0001590
R-HSA-5693571 Nonhomologous End-Joining (NHEJ) 66 2.460174 0.0250763 0.0001590
R-HSA-6783783 Interleukin-10 signaling 34 2.418768 0.0252845 0.0001590
R-HSA-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks 73 2.396526 0.0251252 0.0001590
R-HSA-5693606 DNA Double Strand Break Response 74 2.396061 0.0251318 0.0001590
R-HSA-9006931 Signaling by Nuclear Receptors 244 2.381399 0.0243898 0.0001590
R-HSA-1566948 Elastic fibre formation 43 2.370406 0.0252611 0.0001590
R-HSA-8941326 RUNX2 regulates bone development 30 2.351001 0.0252954 0.0001590
R-HSA-69473 G2/M DNA damage checkpoint 91 2.341737 0.0249683 0.0001590
R-HSA-5693607 Processing of DNA double-strand break ends 94 2.341501 0.0249725 0.0001590
R-HSA-1474244 Extracellular matrix organization 263 2.331853 0.0243579 0.0001590
R-HSA-1266695 Interleukin-7 signaling 33 2.306149 0.0253327 0.0001590
R-HSA-3247509 Chromatin modifying enzymes 259 2.278873 0.0243207 0.0001590
R-HSA-4839726 Chromatin organization 259 2.278873 0.0243207 0.0001590
R-HSA-5693567 HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA) 126 2.235138 0.0248641 0.0001590
R-HSA-157118 Signaling by NOTCH 224 2.214671 0.0244334 0.0001590
R-HSA-8878171 Transcriptional regulation by RUNX1 218 2.201971 0.0244490 0.0001590
R-HSA-5693538 Homology Directed Repair 132 2.171556 0.0248447 0.0001590
R-HSA-3000170 Syndecan interactions 27 2.155250 0.0253136 0.0001590
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins 175 2.093088 0.0245655 0.0001590
R-HSA-1474290 Collagen formation 84 2.086264 0.0250805 0.0001590
R-HSA-201681 TCF dependent signaling in response to WNT 215 2.034284 0.0244125 0.0001590
R-HSA-2990846 SUMOylation 181 2.007948 0.0245606 0.0001590
R-HSA-5693532 DNA Double-Strand Break Repair 160 1.923506 0.0246523 0.0001590
R-HSA-195258 RHO GTPase Effectors 304 1.840488 0.0241978 0.0001590
R-HSA-449147 Signaling by Interleukins 393 1.805721 0.0238851 0.0001590
R-HSA-195721 Signaling by WNT 309 1.690092 0.0484043 0.0002494
R-HSA-68886 M Phase 370 1.647770 0.0479453 0.0002489
R-HSA-2262752 Cellular responses to stress 405 1.632674 0.0477761 0.0002489
Enriched terms for module #EE8045 (MTcor = 0.93)
ID Description setSize NES p.adjust qvalues
R-HSA-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 59 3.428710 0.0224452 0.0001374
R-HSA-5334118 DNA methylation 57 3.406522 0.0225278 0.0001374
R-HSA-73728 RNA Polymerase I Promoter Opening 57 3.355613 0.0225278 0.0001374
R-HSA-2299718 Condensation of Prophase Chromosomes 66 3.267881 0.0222082 0.0001374
R-HSA-427359 SIRT1 negatively regulates rRNA expression 62 3.259000 0.0223359 0.0001374
R-HSA-212300 PRC2 methylates histones and DNA 67 3.195257 0.0221954 0.0001374
R-HSA-3214815 HDACs deacetylate histones 89 3.183673 0.0217741 0.0001374
R-HSA-912446 Meiotic recombination 77 3.177327 0.0220402 0.0001374
R-HSA-1912408 Pre-NOTCH Transcription and Translation 87 3.167742 0.0218376 0.0001374
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression 70 3.166898 0.0221338 0.0001374
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function 87 3.142486 0.0218376 0.0001374
R-HSA-5625740 RHO GTPases activate PKNs 87 3.092663 0.0218376 0.0001374
R-HSA-1500620 Meiosis 106 3.041621 0.0214335 0.0001374
R-HSA-171306 Packaging Of Telomere Ends 45 3.029616 0.0228412 0.0001374
R-HSA-73772 RNA Polymerase I Promoter Escape 85 3.024781 0.0218633 0.0001374
R-HSA-1221632 Meiotic synapsis 69 3.021587 0.0221711 0.0001374
R-HSA-1912422 Pre-NOTCH Expression and Processing 103 2.995518 0.0214362 0.0001374
R-HSA-1474165 Reproduction 121 2.990888 0.0211577 0.0001374
R-HSA-977225 Amyloid fiber formation 92 2.976874 0.0216948 0.0001374
R-HSA-110330 Recognition and association of DNA glycosylase with site containing an affected purine 49 2.955917 0.0227469 0.0001374
R-HSA-110331 Cleavage of the damaged purine 49 2.955917 0.0227469 0.0001374
R-HSA-73927 Depurination 49 2.955917 0.0227469 0.0001374
R-HSA-5250924 B-WICH complex positively regulates rRNA expression 85 2.945840 0.0218633 0.0001374
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex 83 2.931072 0.0218740 0.0001374
R-HSA-2559582 Senescence-Associated Secretory Phenotype (SASP) 103 2.919696 0.0214362 0.0001374
R-HSA-427413 NoRC negatively regulates rRNA expression 100 2.872722 0.0214971 0.0001374
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis 105 2.867060 0.0214081 0.0001374
R-HSA-5619507 Activation of HOX genes during differentiation 105 2.867060 0.0214081 0.0001374
R-HSA-5578749 Transcriptional regulation by small RNAs 100 2.865456 0.0214971 0.0001374
R-HSA-9018519 Estrogen-dependent gene expression 139 2.861305 0.0208499 0.0001374
R-HSA-110328 Recognition and association of DNA glycosylase with site containing an affected pyrimidine 54 2.857918 0.0225696 0.0001374
R-HSA-110329 Cleavage of the damaged pyrimidine 54 2.857918 0.0225696 0.0001374
R-HSA-73928 Depyrimidination 54 2.857918 0.0225696 0.0001374
R-HSA-2559586 DNA Damage/Telomere Stress Induced Senescence 72 2.845834 0.0220842 0.0001374
R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere 67 2.832629 0.0221954 0.0001374
R-HSA-774815 Nucleosome assembly 67 2.832629 0.0221954 0.0001374
R-HSA-73929 Base-Excision Repair, AP Site Formation 56 2.824304 0.0225502 0.0001374
R-HSA-5250941 Negative epigenetic regulation of rRNA expression 103 2.813435 0.0214362 0.0001374
R-HSA-3214842 HDMs demethylate histones 50 2.792860 0.0227196 0.0001374
R-HSA-73864 RNA Polymerase I Transcription 105 2.772099 0.0214081 0.0001374
R-HSA-73854 RNA Polymerase I Promoter Clearance 104 2.753275 0.0214122 0.0001374
R-HSA-5250913 Positive epigenetic regulation of rRNA expression 100 2.745753 0.0214971 0.0001374
R-HSA-3214858 RMTs methylate histone arginines 74 2.745707 0.0220896 0.0001374
R-HSA-3214847 HATs acetylate histones 134 2.695651 0.0209365 0.0001374
R-HSA-68875 Mitotic Prophase 134 2.687889 0.0209365 0.0001374
R-HSA-157579 Telomere Maintenance 74 2.678335 0.0220896 0.0001374
R-HSA-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks 73 2.669142 0.0220969 0.0001374
R-HSA-5693606 DNA Double Strand Break Response 74 2.658132 0.0220896 0.0001374
R-HSA-211000 Gene Silencing by RNA 128 2.636333 0.0209926 0.0001374
R-HSA-5693571 Nonhomologous End-Joining (NHEJ) 66 2.633793 0.0222082 0.0001374
R-HSA-3214841 PKMTs methylate histone lysines 68 2.560910 0.0221843 0.0001374
R-HSA-212165 Epigenetic regulation of gene expression 140 2.555835 0.0208463 0.0001374
R-HSA-2559580 Oxidative Stress Induced Senescence 116 2.542884 0.0212351 0.0001374
R-HSA-73886 Chromosome Maintenance 101 2.490931 0.0215019 0.0001374
R-HSA-73884 Base Excision Repair 84 2.481520 0.0218801 0.0001374
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs 120 2.458849 0.0211600 0.0001374
R-HSA-8939211 ESR-mediated signaling 205 2.449368 0.0200212 0.0001374
R-HSA-69473 G2/M DNA damage checkpoint 91 2.394096 0.0217515 0.0001374
R-HSA-5693607 Processing of DNA double-strand break ends 94 2.388162 0.0216587 0.0001374
R-HSA-3247509 Chromatin modifying enzymes 259 2.382042 0.0195119 0.0001374
R-HSA-4839726 Chromatin organization 259 2.382042 0.0195119 0.0001374
R-HSA-1474290 Collagen formation 84 2.337750 0.0218801 0.0001374
R-HSA-2559583 Cellular Senescence 183 2.295883 0.0202788 0.0001374
R-HSA-8878171 Transcriptional regulation by RUNX1 218 2.261105 0.0198763 0.0001374
R-HSA-2022090 Assembly of collagen fibrils and other multimeric structures 56 2.236997 0.0225502 0.0001374
R-HSA-5693567 HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA) 126 2.229659 0.0210738 0.0001374
R-HSA-6785807 Interleukin-4 and Interleukin-13 signaling 88 2.229070 0.0218120 0.0001374
R-HSA-9006931 Signaling by Nuclear Receptors 244 2.206897 0.0196781 0.0001374
R-HSA-1474244 Extracellular matrix organization 263 2.206092 0.0194762 0.0001374
R-HSA-1650814 Collagen biosynthesis and modifying enzymes 65 2.192422 0.0222185 0.0001374
R-HSA-5693538 Homology Directed Repair 132 2.149519 0.0210048 0.0001374
R-HSA-216083 Integrin cell surface interactions 75 2.089222 0.0220449 0.0001374
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins 175 2.071740 0.0203379 0.0001374
R-HSA-4551638 SUMOylation of chromatin organization proteins 70 2.046488 0.0442675 0.0001501
R-HSA-5693532 DNA Double-Strand Break Repair 160 2.018206 0.0205764 0.0001374
R-HSA-2990846 SUMOylation 181 1.979695 0.0202852 0.0001374
R-HSA-157118 Signaling by NOTCH 224 1.951114 0.0198181 0.0001374
R-HSA-1474228 Degradation of the extracellular matrix 117 1.880459 0.0424171 0.0001454
R-HSA-195258 RHO GTPase Effectors 304 1.829443 0.0191205 0.0001374
R-HSA-194315 Signaling by Rho GTPases 427 1.815317 0.0183115 0.0001374
R-HSA-201681 TCF dependent signaling in response to WNT 215 1.685616 0.0398614 0.0001399
R-HSA-449147 Signaling by Interleukins 393 1.646806 0.0185323 0.0001374
R-HSA-68886 M Phase 370 1.603246 0.0186825 0.0001374
Enriched terms for module #00B9E3 (MTcor = -0.93)
ID Description setSize NES p.adjust qvalues
R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 122 2.771562 0.0197786 0.0003057
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport 170 2.722842 0.0189276 0.0003057
R-HSA-611105 Respiratory electron transport 100 2.712848 0.0202396 0.0003057
R-HSA-112316 Neuronal System 379 2.643595 0.0169280 0.0003057
R-HSA-112315 Transmission across Chemical Synapses 245 2.572379 0.0179982 0.0003057
R-HSA-180024 DARPP-32 events 25 2.566180 0.0231774 0.0003057
R-HSA-5576892 Phase 0 - rapid depolarisation 45 2.542660 0.0219888 0.0003057
R-HSA-1296072 Voltage gated Potassium channels 40 2.533345 0.0222219 0.0003057
R-HSA-399719 Trafficking of AMPA receptors 30 2.525597 0.0228369 0.0003057
R-HSA-399721 Glutamate binding, activation of AMPA receptors and synaptic plasticity 30 2.525597 0.0228369 0.0003057
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission 184 2.501833 0.0187214 0.0003057
R-HSA-6799198 Complex I biogenesis 55 2.486575 0.0215979 0.0003057
R-HSA-442755 Activation of NMDA receptors and postsynaptic events 84 2.413330 0.0206268 0.0003057
R-HSA-438066 Unblocking of NMDA receptors, glutamate binding and activation 22 2.398864 0.0233726 0.0003057
R-HSA-445095 Interaction between L1 and Ankyrins 29 2.389660 0.0228525 0.0003057
R-HSA-442982 Ras activation upon Ca2+ influx through NMDA receptor 21 2.358380 0.0234935 0.0003057
R-HSA-9620244 Long-term potentiation 24 2.331833 0.0231806 0.0003057
R-HSA-9617324 Negative regulation of NMDA receptor-mediated neuronal transmission 22 2.316670 0.0233726 0.0003057
R-HSA-438064 Post NMDA receptor activation events 73 2.314038 0.0210213 0.0003057
R-HSA-5682910 LGI-ADAM interactions 14 2.302572 0.0241829 0.0003057
R-HSA-416993 Trafficking of GluR2-containing AMPA receptors 16 2.294111 0.0239491 0.0003057
R-HSA-6794362 Protein-protein interactions at synapses 87 2.281273 0.0205509 0.0003057
R-HSA-1489509 DAG and IP3 signaling 41 2.253555 0.0221843 0.0003057
R-HSA-111933 Calmodulin induced events 35 2.244918 0.0224995 0.0003057
R-HSA-111997 CaM pathway 35 2.244918 0.0224995 0.0003057
R-HSA-8849932 Synaptic adhesion-like molecules 21 2.236925 0.0469870 0.0004354
R-HSA-1296071 Potassium Channels 92 2.209534 0.0204446 0.0003057
R-HSA-168799 Neurotoxicity of clostridium toxins 10 2.193865 0.0494018 0.0004437
R-HSA-442742 CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling 29 2.190215 0.0228525 0.0003057
R-HSA-5576891 Cardiac conduction 131 2.186421 0.0196061 0.0003057
R-HSA-5339562 Uptake and actions of bacterial toxins 30 2.186355 0.0228369 0.0003057
R-HSA-111885 Opioid Signalling 86 2.173169 0.0205528 0.0003057
R-HSA-111996 Ca-dependent events 37 2.168548 0.0447450 0.0004302
R-HSA-1168372 Downstream signaling events of B Cell Receptor (BCR) 81 2.166032 0.0207344 0.0003057
R-HSA-888590 GABA synthesis, release, reuptake and degradation 19 2.161818 0.0472005 0.0004354
R-HSA-442720 CREB1 phosphorylation through the activation of Adenylate Cyclase 13 2.151123 0.0484717 0.0004412
R-HSA-1236978 Cross-presentation of soluble exogenous antigens (endosomes) 47 2.149661 0.0219284 0.0003057
R-HSA-210500 Glutamate Neurotransmitter Release Cycle 24 2.146751 0.0463612 0.0004354
R-HSA-69052 Switching of origins to a post-replicative state 87 2.142347 0.0205509 0.0003057
R-HSA-5578775 Ion homeostasis 53 2.140474 0.0216580 0.0003057
R-HSA-68827 CDT1 association with the CDC6:ORC:origin complex 57 2.130876 0.0215175 0.0003057
R-HSA-68867 Assembly of the pre-replicative complex 65 2.128218 0.0212570 0.0003057
R-HSA-5610783 Degradation of GLI2 by the proteasome 57 2.115002 0.0215175 0.0003057
R-HSA-112310 Neurotransmitter release cycle 47 2.106833 0.0219284 0.0003057
R-HSA-8986944 Transcriptional Regulation by MECP2 61 2.090800 0.0213952 0.0003057
R-HSA-5610785 GLI3 is processed to GLI3R by the proteasome 57 2.082944 0.0215175 0.0003057
R-HSA-2454202 Fc epsilon receptor (FCERI) signaling 129 2.079485 0.0196412 0.0003057
R-HSA-68949 Orc1 removal from chromatin 69 2.077892 0.0210941 0.0003057
R-HSA-5610780 Degradation of GLI1 by the proteasome 57 2.075156 0.0215175 0.0003057
R-HSA-5676590 NIK–>noncanonical NF-kB signaling 56 2.066272 0.0215590 0.0003057
R-HSA-174113 SCF-beta-TrCP mediated degradation of Emi1 53 2.034135 0.0216580 0.0003057
R-HSA-8939902 Regulation of RUNX2 expression and activity 70 2.018323 0.0421516 0.0004217
R-HSA-174084 Autodegradation of Cdh1 by Cdh1:APC/C 62 2.018057 0.0427044 0.0004217
R-HSA-176408 Regulation of APC/C activators between G1/S and early anaphase 76 2.013606 0.0418253 0.0004217
R-HSA-6794361 Neurexins and neuroligins 56 2.008824 0.0431180 0.0004217
R-HSA-5607761 Dectin-1 mediated noncanonical NF-kB signaling 57 2.008410 0.0430349 0.0004217
R-HSA-5610787 Hedgehog ‘off’ state 108 2.001968 0.0200302 0.0003057
R-HSA-9604323 Negative regulation of NOTCH4 signaling 54 1.999309 0.0432453 0.0004217
R-HSA-983705 Signaling by the B Cell Receptor (BCR) 107 1.998265 0.0200599 0.0003057
R-HSA-69017 CDK-mediated phosphorylation and removal of Cdc6 69 1.989499 0.0421881 0.0004217
R-HSA-373760 L1CAM interactions 111 1.940906 0.0399737 0.0004217
R-HSA-5607764 CLEC7A (Dectin-1) signaling 98 1.921267 0.0406331 0.0004217
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation 296 1.889138 0.0175230 0.0003057
R-HSA-5673001 RAF/MAP kinase cascade 224 1.863297 0.0181937 0.0003057
R-HSA-397014 Muscle contraction 187 1.841178 0.0187025 0.0003057
R-HSA-5684996 MAPK1/MAPK3 signaling 230 1.806671 0.0181680 0.0003057
R-HSA-8951664 Neddylation 225 1.772501 0.0363849 0.0004217
R-HSA-5683057 MAPK family signaling cascades 266 1.739480 0.0177747 0.0003057
R-HSA-1852241 Organelle biogenesis and maintenance 286 1.730102 0.0176001 0.0003057
R-HSA-69620 Cell Cycle Checkpoints 279 1.688245 0.0176632 0.0003057
Enriched terms for module #84AD00 (MTcor = -0.93)
ID Description setSize NES p.adjust qvalues
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport 170 3.030448 0.0256882 0.0002955
R-HSA-611105 Respiratory electron transport 100 2.953639 0.0261010 0.0002955
R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 122 2.931129 0.0258897 0.0002955
R-HSA-5576892 Phase 0 - rapid depolarisation 45 2.640552 0.0265488 0.0002955
R-HSA-6799198 Complex I biogenesis 55 2.632292 0.0265415 0.0002955
R-HSA-888590 GABA synthesis, release, reuptake and degradation 19 2.531137 0.0269022 0.0002955
R-HSA-71406 Pyruvate metabolism and Citric Acid (TCA) cycle 52 2.519440 0.0265678 0.0002955
R-HSA-71403 Citric acid cycle (TCA cycle) 22 2.480228 0.0268220 0.0002955
R-HSA-112316 Neuronal System 379 2.473304 0.0247369 0.0002955
R-HSA-1296072 Voltage gated Potassium channels 40 2.452507 0.0265594 0.0002955
R-HSA-399719 Trafficking of AMPA receptors 30 2.429160 0.0266492 0.0002955
R-HSA-399721 Glutamate binding, activation of AMPA receptors and synaptic plasticity 30 2.429160 0.0266492 0.0002955
R-HSA-1268020 Mitochondrial protein import 63 2.427393 0.0263920 0.0002955
R-HSA-5682910 LGI-ADAM interactions 14 2.425477 0.0269563 0.0002955
R-HSA-112315 Transmission across Chemical Synapses 245 2.416597 0.0253870 0.0002955
R-HSA-180024 DARPP-32 events 25 2.406851 0.0267465 0.0002955
R-HSA-442982 Ras activation upon Ca2+ influx through NMDA receptor 21 2.375977 0.0268801 0.0002955
R-HSA-5339562 Uptake and actions of bacterial toxins 30 2.311167 0.0266492 0.0002955
R-HSA-112310 Neurotransmitter release cycle 47 2.301053 0.0265631 0.0002955
R-HSA-442755 Activation of NMDA receptors and postsynaptic events 84 2.242816 0.0262123 0.0002955
R-HSA-5389840 Mitochondrial translation elongation 86 2.235272 0.0262236 0.0002955
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission 184 2.229291 0.0255794 0.0002955
R-HSA-111933 Calmodulin induced events 35 2.223602 0.0266275 0.0002955
R-HSA-111997 CaM pathway 35 2.223602 0.0266275 0.0002955
R-HSA-5368287 Mitochondrial translation 92 2.210952 0.0261086 0.0002955
R-HSA-5368286 Mitochondrial translation initiation 86 2.170356 0.0262236 0.0002955
R-HSA-5419276 Mitochondrial translation termination 86 2.166536 0.0262236 0.0002955
R-HSA-351202 Metabolism of polyamines 83 2.144309 0.0261657 0.0002955
R-HSA-111885 Opioid Signalling 86 2.136095 0.0262236 0.0002955
R-HSA-438064 Post NMDA receptor activation events 73 2.114563 0.0262900 0.0002955
R-HSA-1296071 Potassium Channels 92 2.093680 0.0261086 0.0002955
R-HSA-9609507 Protein localization 158 2.020541 0.0258224 0.0002955
R-HSA-5628897 TP53 Regulates Metabolic Genes 84 1.970919 0.0262123 0.0002955
R-HSA-8951664 Neddylation 225 1.969353 0.0254564 0.0002955
R-HSA-5576891 Cardiac conduction 131 1.937803 0.0258647 0.0002955
R-HSA-163685 Integration of energy metabolism 101 1.905819 0.0260721 0.0002955
R-HSA-8856688 Golgi-to-ER retrograde transport 124 1.869820 0.0258747 0.0002955
R-HSA-5610787 Hedgehog ‘off’ state 108 1.864307 0.0259791 0.0002955
R-HSA-1852241 Organelle biogenesis and maintenance 286 1.728487 0.0252216 0.0002955

Gene Ontology

print_results(enrichment_GO)

No enrichment found for module #73B000

No enrichment found for module #EE8045

No enrichment found for module #00B9E3

No enrichment found for module #84AD00

Disease Ontology

print_results(enrichment_DO)
Enriched terms for module #73B000 (MTcor = 0.94)
ID Description setSize NES p.adjust qvalues
DOID:1936 atherosclerosis 280 2.328354 0.0141355 0.0000646
DOID:1115 sarcoma 173 2.326923 0.0143437 0.0000646
DOID:2348 arteriosclerotic cardiovascular disease 281 2.319477 0.0141406 0.0000646
DOID:2349 arteriosclerosis 287 2.304857 0.0141348 0.0000646
DOID:2213 hemorrhagic disease 121 2.270698 0.0145040 0.0000646
DOID:0050161 lower respiratory tract disease 391 2.258512 0.0139636 0.0000646
DOID:552 pneumonia 78 2.257550 0.0146515 0.0000646
DOID:3770 pulmonary fibrosis 101 2.254562 0.0145592 0.0000646
DOID:1579 respiratory system disease 429 2.239237 0.0138906 0.0000646
DOID:850 lung disease 383 2.238401 0.0139628 0.0000646
DOID:3083 chronic obstructive pulmonary disease 174 2.222449 0.0143482 0.0000646
DOID:3717 gastric adenocarcinoma 81 2.214898 0.0146567 0.0000646
DOID:2218 blood platelet disease 76 2.212813 0.0146649 0.0000646
DOID:5520 head and neck squamous cell carcinoma 153 2.211620 0.0143988 0.0000646
DOID:3082 interstitial lung disease 136 2.199707 0.0145166 0.0000646
DOID:2320 obstructive lung disease 229 2.198971 0.0142248 0.0000646
DOID:7148 rheumatoid arthritis 430 2.196661 0.0138820 0.0000646
DOID:10534 stomach cancer 231 2.187767 0.0142008 0.0000646
DOID:13133 HELLP syndrome 15 2.169495 0.0300954 0.0001198
DOID:4330 non-langerhans-cell histiocytosis 11 2.167417 0.0300395 0.0001198
DOID:520 aortic disease 48 2.155743 0.0295192 0.0001198
DOID:1247 blood coagulation disease 142 2.155103 0.0144770 0.0000646
DOID:11934 head and neck cancer 209 2.151208 0.0142719 0.0000646
DOID:104 bacterial infectious disease 191 2.144434 0.0143042 0.0000646
DOID:14504 Niemann-Pick disease 10 2.141539 0.0300544 0.0001198
DOID:3627 aortic aneurysm 47 2.130650 0.0443138 0.0001681
DOID:1542 head and neck carcinoma 206 2.128565 0.0143157 0.0000646
DOID:37 skin disease 254 2.125717 0.0141908 0.0000646
DOID:1793 pancreatic cancer 276 2.111636 0.0141465 0.0000646
DOID:1588 thrombocytopenia 57 2.110410 0.0294471 0.0001198
DOID:4362 cervical cancer 96 2.106032 0.0145975 0.0000646
DOID:1520 colon carcinoma 149 2.105316 0.0144346 0.0000646
DOID:409 liver disease 500 2.104661 0.0137786 0.0000646
DOID:5517 stomach carcinoma 133 2.103167 0.0145019 0.0000646
DOID:201 connective tissue cancer 338 2.099796 0.0140341 0.0000646
DOID:4905 pancreatic carcinoma 206 2.098585 0.0143157 0.0000646
DOID:4481 allergic rhinitis 67 2.096063 0.0146891 0.0000646
DOID:1176 bronchial disease 104 2.091506 0.0145449 0.0000646
DOID:824 periodontitis 88 2.090860 0.0146400 0.0000646
DOID:3326 purpura 57 2.087347 0.0294471 0.0001198
DOID:2893 cervix carcinoma 95 2.083596 0.0145964 0.0000646
DOID:2163 nasal cavity disease 69 2.078487 0.0147015 0.0000646
DOID:2825 nose disease 69 2.078487 0.0147015 0.0000646
DOID:4483 rhinitis 69 2.078487 0.0147015 0.0000646
DOID:3388 periodontal disease 99 2.072415 0.0145655 0.0000646
DOID:0050338 primary bacterial infectious disease 165 2.071690 0.0144081 0.0000646
DOID:170 endocrine gland cancer 443 2.066980 0.0138445 0.0000646
DOID:854 collagen disease 159 2.056954 0.0144179 0.0000646
DOID:10124 corneal disease 46 2.055284 0.0443707 0.0001681
DOID:2151 malignant ovarian surface epithelial-stromal neoplasm 256 2.041443 0.0142160 0.0000646
DOID:2152 ovary epithelial cancer 256 2.041443 0.0142160 0.0000646
DOID:4001 ovarian carcinoma 256 2.041443 0.0142160 0.0000646
DOID:0060100 musculoskeletal system cancer 395 2.035164 0.0139410 0.0000646
DOID:219 colon cancer 252 2.034711 0.0142155 0.0000646
DOID:0060058 lymphoma 66 2.031428 0.0146775 0.0000646
DOID:9256 colorectal cancer 256 2.031151 0.0142160 0.0000646
DOID:3310 atopic dermatitis 92 2.031063 0.0145779 0.0000646
DOID:120 female reproductive organ cancer 393 2.029211 0.0139514 0.0000646
DOID:5672 large intestine cancer 257 2.029211 0.0141949 0.0000646
DOID:4960 bone marrow cancer 274 2.021302 0.0141557 0.0000646
DOID:9538 multiple myeloma 221 2.020293 0.0142745 0.0000646
DOID:16 integumentary system disease 288 2.020174 0.0141139 0.0000646
DOID:6713 cerebrovascular disease 98 2.015214 0.0145836 0.0000646
DOID:1091 tooth disease 114 2.013934 0.0145609 0.0000646
DOID:2237 hepatitis 345 2.011724 0.0140208 0.0000646
DOID:0070004 myeloma 269 2.010450 0.0141805 0.0000646
DOID:399 tuberculosis 106 2.009155 0.0145344 0.0000646
DOID:3910 lung adenocarcinoma 153 1.998887 0.0143988 0.0000646
DOID:2394 ovarian cancer 276 1.993121 0.0141465 0.0000646
DOID:2916 hypersensitivity reaction type IV disease 70 1.987438 0.0440994 0.0001681
DOID:1612 breast cancer 451 1.987036 0.0138379 0.0000646
DOID:5093 thoracic cancer 451 1.987036 0.0138379 0.0000646
DOID:1575 rheumatic disease 147 1.985583 0.0144391 0.0000646
DOID:418 systemic scleroderma 147 1.985583 0.0144391 0.0000646
DOID:419 scleroderma 147 1.985583 0.0144391 0.0000646
DOID:10155 intestinal cancer 268 1.978959 0.0141867 0.0000646
DOID:5082 liver cirrhosis 173 1.977049 0.0143437 0.0000646
DOID:3908 non-small cell lung carcinoma 370 1.971734 0.0139860 0.0000646
DOID:3905 lung carcinoma 441 1.967848 0.0138396 0.0000646
DOID:11054 urinary bladder cancer 90 1.964252 0.0146427 0.0000646
DOID:10283 prostate cancer 364 1.960564 0.0140005 0.0000646
DOID:2043 hepatitis B 160 1.945112 0.0144059 0.0000646
DOID:4074 pancreas adenocarcinoma 142 1.942827 0.0144770 0.0000646
DOID:1040 chronic lymphocytic leukemia 167 1.934531 0.0143951 0.0000646
DOID:2723 dermatitis 123 1.928381 0.0145148 0.0000646
DOID:974 upper respiratory tract disease 86 1.928198 0.0437573 0.0001681
DOID:5041 esophageal cancer 127 1.904152 0.0145341 0.0000646
DOID:8398 osteoarthritis 158 1.902832 0.0144264 0.0000646
DOID:8692 myeloid leukemia 124 1.902192 0.0145242 0.0000646
DOID:2841 asthma 91 1.898807 0.0292472 0.0001198
DOID:10952 nephritis 118 1.888222 0.0290483 0.0001198
DOID:417 hypersensitivity reaction type II disease 444 1.887243 0.0138447 0.0000646
DOID:403 mouth disease 136 1.887171 0.0290333 0.0001198
DOID:3856 male reproductive organ cancer 372 1.886447 0.0139778 0.0000646
DOID:184 bone cancer 224 1.885886 0.0142564 0.0000646
DOID:3393 coronary artery disease 268 1.885598 0.0141867 0.0000646
DOID:3347 osteosarcoma 204 1.880283 0.0142974 0.0000646
DOID:688 embryonal cancer 316 1.871146 0.0140769 0.0000646
DOID:114 heart disease 420 1.870466 0.0138783 0.0000646
DOID:5844 myocardial infarction 220 1.868891 0.0142691 0.0000646
DOID:3459 breast carcinoma 339 1.854647 0.0140220 0.0000646
DOID:4451 renal carcinoma 328 1.853181 0.0140582 0.0000646
DOID:1883 hepatitis C 190 1.846083 0.0143147 0.0000646
DOID:4195 hyperglycemia 110 1.840590 0.0436801 0.0001681
DOID:2994 germ cell cancer 343 1.836173 0.0140100 0.0000646
DOID:3996 urinary system cancer 426 1.831902 0.0138683 0.0000646
DOID:9352 type 2 diabetes mellitus 166 1.831581 0.0288363 0.0001198
DOID:1492 eye and adnexa disease 441 1.829360 0.0138396 0.0000646
DOID:4766 embryoma 298 1.828122 0.0141147 0.0000646
DOID:5614 eye disease 432 1.813335 0.0138781 0.0000646
DOID:0050155 sensory system disease 489 1.786407 0.0138079 0.0000646
DOID:557 kidney disease 374 1.766649 0.0139798 0.0000646
DOID:0060072 benign neoplasm 474 1.760866 0.0138142 0.0000646
DOID:263 kidney cancer 375 1.760670 0.0139738 0.0000646
DOID:4450 renal cell carcinoma 294 1.752802 0.0141368 0.0000646
DOID:1037 lymphoblastic leukemia 359 1.746446 0.0140083 0.0000646
DOID:18 urinary system disease 387 1.742797 0.0139544 0.0000646
DOID:0060084 cell type benign neoplasm 396 1.717393 0.0139259 0.0000646
DOID:74 hematopoietic system disease 366 1.664221 0.0140083 0.0000646
DOID:657 adenoma 278 1.656929 0.0424373 0.0001676
DOID:0050736 autosomal dominant disease 360 1.620271 0.0140068 0.0000646
DOID:3093 nervous system cancer 499 1.618691 0.0137836 0.0000646
DOID:10763 hypertension 482 1.580088 0.0275518 0.0001198
Enriched terms for module #EE8045 (MTcor = 0.93)
ID Description setSize NES p.adjust qvalues
DOID:7148 rheumatoid arthritis 430 2.406930 0.0106781 0.0000717
DOID:3083 chronic obstructive pulmonary disease 174 2.354784 0.0119021 0.0000717
DOID:2213 hemorrhagic disease 121 2.315706 0.0123496 0.0000717
DOID:1588 thrombocytopenia 57 2.284217 0.0130870 0.0000717
DOID:3770 pulmonary fibrosis 101 2.278557 0.0125472 0.0000717
DOID:0050161 lower respiratory tract disease 391 2.276961 0.0108113 0.0000717
DOID:1579 respiratory system disease 429 2.273814 0.0106829 0.0000717
DOID:2320 obstructive lung disease 229 2.272892 0.0115597 0.0000717
DOID:850 lung disease 383 2.266257 0.0108398 0.0000717
DOID:1247 blood coagulation disease 142 2.265142 0.0121645 0.0000717
DOID:9446 cholangitis 25 2.255001 0.0138001 0.0000749
DOID:3388 periodontal disease 99 2.231499 0.0125639 0.0000717
DOID:3082 interstitial lung disease 136 2.231101 0.0122120 0.0000717
DOID:0060049 autoimmune disease of urogenital tract 56 2.217154 0.0130863 0.0000717
DOID:12236 primary biliary cirrhosis 56 2.217154 0.0130863 0.0000717
DOID:9074 systemic lupus erythematosus 58 2.217005 0.0130850 0.0000717
DOID:1115 sarcoma 173 2.209575 0.0118957 0.0000717
DOID:3326 purpura 57 2.205286 0.0261739 0.0001338
DOID:2218 blood platelet disease 76 2.203795 0.0128457 0.0000717
DOID:4481 allergic rhinitis 67 2.201114 0.0129694 0.0000717
DOID:1040 chronic lymphocytic leukemia 167 2.196968 0.0119612 0.0000717
DOID:2163 nasal cavity disease 69 2.192375 0.0129535 0.0000717
DOID:2825 nose disease 69 2.192375 0.0129535 0.0000717
DOID:4483 rhinitis 69 2.192375 0.0129535 0.0000717
DOID:824 periodontitis 88 2.192074 0.0126812 0.0000717
DOID:2916 hypersensitivity reaction type IV disease 70 2.178799 0.0129258 0.0000717
DOID:8857 lupus erythematosus 62 2.165345 0.0130310 0.0000717
DOID:974 upper respiratory tract disease 86 2.150957 0.0127097 0.0000717
DOID:1091 tooth disease 114 2.150849 0.0124174 0.0000717
DOID:11335 sarcoidosis 66 2.149124 0.0259538 0.0001338
DOID:8398 osteoarthritis 158 2.148051 0.0120238 0.0000717
DOID:1176 bronchial disease 104 2.147108 0.0124946 0.0000717
DOID:1936 atherosclerosis 280 2.132366 0.0112663 0.0000717
DOID:2348 arteriosclerotic cardiovascular disease 281 2.129309 0.0112619 0.0000717
DOID:2473 opportunistic mycosis 27 2.125544 0.0411613 0.0001937
DOID:10952 nephritis 118 2.119637 0.0123714 0.0000717
DOID:2349 arteriosclerosis 287 2.118736 0.0112205 0.0000717
DOID:552 pneumonia 78 2.099390 0.0128142 0.0000717
DOID:2841 asthma 91 2.077346 0.0126525 0.0000717
DOID:8692 myeloid leukemia 124 2.072009 0.0123179 0.0000717
DOID:612 primary immunodeficiency disease 158 2.064591 0.0120238 0.0000717
DOID:11934 head and neck cancer 209 2.061705 0.0116792 0.0000717
DOID:1542 head and neck carcinoma 206 2.054663 0.0116903 0.0000717
DOID:0060058 lymphoma 66 2.051627 0.0389307 0.0001848
DOID:399 tuberculosis 106 2.049425 0.0125026 0.0000717
DOID:9538 multiple myeloma 221 2.039118 0.0116078 0.0000717
DOID:9741 biliary tract disease 71 2.036162 0.0387428 0.0001848
DOID:104 bacterial infectious disease 191 2.030575 0.0117797 0.0000717
DOID:12361 Graves’ disease 63 2.028658 0.0260517 0.0001338
DOID:5082 liver cirrhosis 173 2.025518 0.0118957 0.0000717
DOID:5520 head and neck squamous cell carcinoma 153 2.018823 0.0120762 0.0000717
DOID:11054 urinary bladder cancer 90 2.014636 0.0126652 0.0000717
DOID:4138 bile duct disease 70 2.007146 0.0387773 0.0001848
DOID:37 skin disease 254 1.996581 0.0114104 0.0000717
DOID:417 hypersensitivity reaction type II disease 444 1.993203 0.0106488 0.0000717
DOID:4960 bone marrow cancer 274 1.990757 0.0112936 0.0000717
DOID:0070004 myeloma 269 1.988499 0.0113169 0.0000717
DOID:403 mouth disease 136 1.988237 0.0122120 0.0000717
DOID:1037 lymphoblastic leukemia 359 1.980895 0.0109087 0.0000717
DOID:10534 stomach cancer 231 1.962774 0.0115542 0.0000717
DOID:16 integumentary system disease 288 1.961439 0.0112197 0.0000717
DOID:854 collagen disease 159 1.951838 0.0120116 0.0000717
DOID:0050338 primary bacterial infectious disease 165 1.946575 0.0119726 0.0000717
DOID:2723 dermatitis 123 1.942831 0.0123286 0.0000717
DOID:9119 acute myeloid leukemia 93 1.940028 0.0378464 0.0001846
DOID:201 connective tissue cancer 338 1.931140 0.0109980 0.0000717
DOID:1575 rheumatic disease 147 1.923856 0.0121345 0.0000717
DOID:418 systemic scleroderma 147 1.923856 0.0121345 0.0000717
DOID:419 scleroderma 147 1.923856 0.0121345 0.0000717
DOID:5041 esophageal cancer 127 1.918541 0.0123009 0.0000717
DOID:3393 coronary artery disease 268 1.902290 0.0113295 0.0000717
DOID:1520 colon carcinoma 149 1.890664 0.0121177 0.0000717
DOID:409 liver disease 500 1.888508 0.0104810 0.0000717
DOID:526 Human immunodeficiency virus infectious disease 132 1.886409 0.0122519 0.0000717
DOID:170 endocrine gland cancer 443 1.883490 0.0106500 0.0000717
DOID:5844 myocardial infarction 220 1.873768 0.0116060 0.0000717
DOID:10283 prostate cancer 364 1.863541 0.0109001 0.0000717
DOID:1793 pancreatic cancer 276 1.859825 0.0112846 0.0000717
DOID:74 hematopoietic system disease 366 1.854196 0.0108872 0.0000717
DOID:0060100 musculoskeletal system cancer 395 1.852221 0.0107932 0.0000717
DOID:10591 pre-eclampsia 217 1.845411 0.0116364 0.0000717
DOID:5517 stomach carcinoma 133 1.835183 0.0488892 0.0002260
DOID:5683 hereditary breast ovarian cancer 200 1.828842 0.0117111 0.0000717
DOID:688 embryonal cancer 316 1.821178 0.0111069 0.0000717
DOID:3213 demyelinating disease 144 1.820715 0.0364894 0.0001803
DOID:2377 multiple sclerosis 138 1.819929 0.0366201 0.0001803
DOID:9352 type 2 diabetes mellitus 166 1.819645 0.0239338 0.0001260
DOID:2237 hepatitis 345 1.817577 0.0109721 0.0000717
DOID:3856 male reproductive organ cancer 372 1.814937 0.0108669 0.0000717
DOID:219 colon cancer 252 1.812164 0.0114349 0.0000717
DOID:2994 germ cell cancer 343 1.803332 0.0109889 0.0000717
DOID:4766 embryoma 298 1.801106 0.0111856 0.0000717
DOID:9256 colorectal cancer 256 1.800043 0.0113965 0.0000717
DOID:5672 large intestine cancer 257 1.790947 0.0113963 0.0000717
DOID:3996 urinary system cancer 426 1.790153 0.0106907 0.0000717
DOID:18 urinary system disease 387 1.788396 0.0108226 0.0000717
DOID:557 kidney disease 374 1.782717 0.0108602 0.0000717
DOID:4451 renal carcinoma 328 1.781683 0.0110522 0.0000717
DOID:3905 lung carcinoma 441 1.762810 0.0106577 0.0000717
DOID:114 heart disease 420 1.752559 0.0107121 0.0000717
DOID:4905 pancreatic carcinoma 206 1.751490 0.0233807 0.0001243
DOID:1492 eye and adnexa disease 441 1.748146 0.0106577 0.0000717
DOID:10155 intestinal cancer 268 1.747589 0.0113295 0.0000717
DOID:263 kidney cancer 375 1.745672 0.0108610 0.0000717
DOID:3908 non-small cell lung carcinoma 370 1.729466 0.0108690 0.0000717
DOID:120 female reproductive organ cancer 393 1.729094 0.0107987 0.0000717
DOID:184 bone cancer 224 1.727615 0.0231596 0.0001243
DOID:0050155 sensory system disease 489 1.726523 0.0105067 0.0000717
DOID:5614 eye disease 432 1.720764 0.0106620 0.0000717
DOID:1612 breast cancer 451 1.703644 0.0106239 0.0000717
DOID:5093 thoracic cancer 451 1.703644 0.0106239 0.0000717
DOID:15 reproductive system disease 281 1.677028 0.0337858 0.0001695
DOID:0050736 autosomal dominant disease 360 1.669221 0.0109122 0.0000717
DOID:10763 hypertension 482 1.559100 0.0316265 0.0001601
Enriched terms for module #00B9E3 (MTcor = -0.93)
ID Description setSize NES p.adjust qvalues
DOID:2234 focal epilepsy 57 2.205412 0.0252781 0.000262
DOID:1826 epilepsy syndrome 191 2.070965 0.0109172 0.000262
DOID:0060041 autism spectrum disorder 166 1.800904 0.0334385 0.000262
DOID:12849 autistic disorder 166 1.800904 0.0334385 0.000262
DOID:0060040 pervasive developmental disorder 175 1.780626 0.0332072 0.000262
Enriched terms for module #84AD00 (MTcor = -0.93)
ID Description setSize NES p.adjust qvalues
DOID:1826 epilepsy syndrome 191 2.01758 0.0148789 0.000146


Disease Gene Network

print_results(enrichment_DGN)

No enrichment found for module #73B000

Enriched terms for module #EE8045 (MTcor = 0.93)
ID Description setSize NES p.adjust qvalues
umls:C3495559 Juvenile arthritis 272 2.374540 0.0496448 0.0003302
umls:C3714514 Infection 464 2.191351 0.0464164 0.0003302
umls:C0036421 Systemic Scleroderma 441 2.101877 0.0466225 0.0003302
umls:C1800706 Idiopathic Pulmonary Fibrosis 276 2.063431 0.0495485 0.0003302
umls:C0032285 Pneumonia 312 2.046221 0.0488940 0.0003302
umls:C0009319 Colitis 414 2.016902 0.0470188 0.0003302
umls:C0024115 Lung diseases 276 1.993770 0.0495485 0.0003302
umls:C0019829 Hodgkin Disease 306 1.986978 0.0490109 0.0003302
umls:C0032914 Pre-Eclampsia 275 1.982788 0.0495356 0.0003302
umls:C0024305 Lymphoma, Non-Hodgkin 426 1.923352 0.0469401 0.0003302
umls:C0003864 Arthritis 427 1.920451 0.0469112 0.0003302
umls:C0042373 Vascular Diseases 328 1.913508 0.0485818 0.0003302
umls:C0034069 Pulmonary Fibrosis 290 1.904986 0.0492768 0.0003302
umls:C0011615 Dermatitis, Atopic 333 1.867993 0.0485165 0.0003302
umls:C0014072 Experimental Autoimmune Encephalomyelitis 305 1.864136 0.0490439 0.0003302
umls:C0007570 Celiac Disease 268 1.856958 0.0497089 0.0003302
umls:C0376545 Hematologic Neoplasms 399 1.845926 0.0472276 0.0003302
umls:C0153676 Secondary malignant neoplasm of lung 490 1.843747 0.0461331 0.0003302
umls:C3272363 Ischemic Cerebrovascular Accident 271 1.820657 0.0496462 0.0003302
umls:C0023267 Fibroid Tumor 270 1.814286 0.0496866 0.0003302
umls:C0037274 Dermatologic disorders 363 1.807124 0.0478928 0.0003302
umls:C0948008 Ischemic stroke 307 1.799159 0.0489780 0.0003302
umls:C0023895 Liver diseases 446 1.793146 0.0465705 0.0003302
umls:C0021051 Immunologic Deficiency Syndromes 349 1.789369 0.0481426 0.0003302
umls:C0035126 Reperfusion Injury 271 1.770544 0.0496462 0.0003302
umls:C0278996 Cancer of Head and Neck 361 1.768079 0.0479485 0.0003302
umls:C0079744 Diffuse Large B-Cell Lymphoma 459 1.755678 0.0464889 0.0003302
umls:C1292769 Precursor B-cell lymphoblastic leukemia 297 1.753167 0.0491671 0.0003302
umls:C0013595 Eczema 281 1.746958 0.0494791 0.0003302
umls:C1519670 Tumor Angiogenesis 360 1.746787 0.0479512 0.0003302
umls:C0853879 Invasive breast carcinoma 321 1.746492 0.0486779 0.0003302
umls:C0023470 Myeloid Leukemia 430 1.742136 0.0468560 0.0003302
umls:C0409974 Lupus Erythematosus 284 1.737924 0.0494440 0.0003302
umls:C1621958 Glioblastoma Multiforme 370 1.737153 0.0478239 0.0003302
umls:C1378703 Renal carcinoma 387 1.726801 0.0475113 0.0003302
umls:C0029456 Osteoporosis 368 1.710440 0.0478854 0.0003302
umls:C0220641 Lip and Oral Cavity Carcinoma 344 1.705676 0.0482859 0.0003302
umls:C0278883 Metastatic melanoma 272 1.704536 0.0496448 0.0003302
umls:C0153381 Malignant neoplasm of mouth 344 1.703523 0.0482859 0.0003302
umls:C0023493 Adult T-Cell Lymphoma/Leukemia 366 1.691341 0.0478854 0.0003302
umls:C0085110 Severe Combined Immunodeficiency 420 1.683272 0.0469652 0.0003302
umls:C0239946 Fibrosis, Liver 271 1.672850 0.0496462 0.0003302
umls:C0019348 Herpes Simplex Infections 425 1.620043 0.0469427 0.0003302
umls:C0345904 Malignant neoplasm of liver 481 1.618418 0.0461630 0.0003302
umls:C0025286 Meningioma 381 1.609239 0.0476085 0.0003302
umls:C0152018 Esophageal carcinoma 445 1.602814 0.0465977 0.0003302
umls:C0008626 Congenital chromosomal disease 440 1.601495 0.0466313 0.0003302
umls:C0546837 Malignant neoplasm of esophagus 485 1.593860 0.0461717 0.0003302
umls:C0022661 Kidney Failure, Chronic 483 1.589512 0.0461954 0.0003302
Enriched terms for module #00B9E3 (MTcor = -0.93)
ID Description setSize NES p.adjust qvalues
umls:C0004134 Ataxia 221 1.957340 0.0467638 0.0015602
umls:C0014556 Epilepsy, Temporal Lobe 175 1.878511 0.0482947 0.0015602
umls:C0525045 Mood Disorders 238 1.864062 0.0462184 0.0015602
umls:C1510586 Autism Spectrum Disorders 216 1.835349 0.0469588 0.0015602
umls:C1263846 Attention deficit hyperactivity disorder 365 1.706949 0.0435070 0.0015602
umls:C0004936 Mental disorders 384 1.688912 0.0431365 0.0015602

No enrichment found for module #84AD00